Non-biologists often find names given to moulds difficult. The current system of naming fungi (the kingdom to which moulds belong) and other living organisms including plants and animals was introduced by Linnaeus in 1753. In this system (referred to as binomial nomenclature) an organism is identified by 2 names, i.e., the generic name and a specific name. For example, for Aspergillus niger, the generic name is Aspergillus and the specific name (or epithet) is niger. These names may be descriptive or given to commemorate the work of researchers or benefactors, or the place where the fungus was found; thus Aspergillus chevalieri is named after the French mycologist F.F. Chevallier (1796-1840), and Aspergillus amstelodami was originally discovered in Amsterdam. Aspergillus niger is descriptive. It refers to a mould with conidiophores (spore bearing structures) which are swollen at the apex, which produces chains of conidia (spores) and that the fungus is black (Latin: niger), and that it has the appearance of a mop (Latin: aspergillum).

Sometimes a fungus (plural is fungi) may have more than one name. For example Stachybotrys chartarum is still called by some people as Stachybotrys atra. This happens when the name of a fungus is changed. Name changing occurs if the original description of the fungus was inadequate so that the fungus is not recognizable to others and subsequently given new name(s) or through recognizing spurious differences between individuals as taxonomically significant. Much of the duplication is due simply to the enormous body of literature which must be searched through to find previously-published names which may be applied to apparently new species. A fungus may also be referred by more than one name if it exists in different forms (or states). Each form may have a different name.

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